Merging development in ATOF testing

.containers/coatjava.Dockerfile

@@ -22,4 +22,5 @@ ARG REF_NAME=development
 # build coatjava 
 RUN java --version && cd /opt && \
     git clone https://code.jlab.org/hallb/alert/coatjava.git && cd coatjava && \
-    git fetch origin && git checkout ${REF_NAME} && ./build-coatjava.sh --quiet
+    git fetch origin && git checkout ${REF_NAME} && ./build-coatjava.sh --quiet && \
+    ./install-clara /opt/clara

.containers/coatjava.def

@@ -0,0 +1,14 @@
+Bootstrap: docker
+From: codecr.jlab.org/hallb/alert/coatjava/coatjava:{{ REF_NAME }}
+
+
+%environment
+    export CLAS12DIR=/opt/coatjava/coatjava
+
+%help
+    This is a clas12 coatjava container used to run coatjava on HPC systems
+    and do rapid development.
+
+%labels
+    Author Whitney Armstrong [email protected]
+    REF_NAME {{ REF_NAME }}

etc/bankdefs/util/dumpBankIDs.rb → .github/make_banks_readme.rb

@@ -51,13 +51,8 @@
 # dump a table
 puts """# Bank Group and Item IDs
 
-This file was generated by
-```bash
-#{$0} #{ARGV.join ' '}
-```
-
-> [!IMPORTANT]
-> Please re-run this script if you modify any of the bank definitions.
+> [!NOTE]
+> Iguana banks, which are defined in the Iguana repository, use group number 30000.
 
 """
 

.github/make_banks_readme_precommit.sh

@@ -0,0 +1,2 @@
+#!/usr/bin/env sh
+.github/make_banks_readme.rb etc/bankdefs/hipo4 > etc/bankdefs/hipo4/README.md

.gitignore

@@ -32,6 +32,12 @@ hs_err_pid*
 *.iml
 .idea
 
+# eclipse JDT language server
+.classpath
+.factorypath
+.project
+.settings
+
 # no log files:
 *.log
 *.evio 

.gitlab-ci.yml

@@ -9,6 +9,7 @@ workflow:
 
 variables:
   KUBERNETES_MEMORY_LIMIT: "8Gi"
+  REF_NAME: ${CI_COMMIT_REF_NAME}
 
 default:
   image: ubuntu:noble
@@ -69,3 +70,16 @@ shared_for_alert_tests:
     project: hallb/alert/atof/shared_for_alert
     strategy: depend
 
+coatjava:singularity:
+  image: eicweb.phy.anl.gov:4567/containers/image_recipes/ubuntu_dind:latest
+  tags:
+     - silicon
+  allow_failure: true
+  script:
+    - apptainer build  --build-arg REF_NAME=${REF_NAME} coatjava.sif .containers/coatjava.def
+    - ls -lrth
+  artifacts:
+      paths:
+        - coatjava.sif
+
+

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+repos:
+- repo: local
+  hooks:
+    - id: make_banks_readme
+      name: make banks readme
+      entry: .github/make_banks_readme_precommit.sh
+      language: script
+      pass_filenames: false

README.md

@@ -58,3 +58,6 @@ http://stackoverflow.com/questions/600079/how-do-i-clone-a-subdirectory-only-of-
 
 -->
 
+
+[Coatjava Apptainer](https://code.jlab.org/hallb/alert/coatjava/-/jobs/artifacts/development/raw/coatjava.sif?job=coatjava%3Asingularity)
+

common-tools/clara-io/pom.xml

@@ -3,14 +3,14 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clara-io</artifactId>
-  <version>11.1.2-SNAPSHOT</version>
+  <version>12.0.1t-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.1.2-SNAPSHOT</version>
+    <version>12.0.1t-SNAPSHOT</version>
   </parent>
 
   <dependencies>

common-tools/clas-analysis/pom.xml

@@ -3,63 +3,63 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-analysis</artifactId>
-  <version>11.1.2-SNAPSHOT</version>
+  <version>12.0.1t-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.1.2-SNAPSHOT</version>
+    <version>12.0.1t-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-physics</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-jcsg</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>swim-tools</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-detector</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-reco</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
   </dependencies>
 

common-tools/clas-detector/pom.xml

@@ -3,21 +3,21 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-detector</artifactId>
-  <version>11.1.2-SNAPSHOT</version>
+  <version>12.0.1t-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>11.1.2-SNAPSHOT</version>
+    <version>12.0.1t-SNAPSHOT</version>
   </parent>
 
   <dependencies>
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
 
     <dependency>
@@ -29,13 +29,13 @@
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>11.1.2-SNAPSHOT</version>
+      <version>12.0.1t-SNAPSHOT</version>
     </dependency>
   </dependencies>
 

common-tools/clas-detector/src/main/java/org/jlab/detector/banks/RawBank.java

@@ -74,9 +74,9 @@ public static enum OrderType {
         BGADDED_NOISE1  ( 70),  // background hits retained by level-1 denoising
         BGADDED_NOISE2  ( 80),  // background hits retained by level-2 denoising
         BGADDED_NOISE3  ( 90),  // background hits retained by level-3 denoising
-        USER1           (100),
-        USER2           (110),
-        USER3           (120);
+        DECREMOVED      (100),  // hits removed during decoding
+        USER1           (110),
+        USER2           (120);
         private final int rawOrderId;
         private OrderType(int id){ rawOrderId = id; }
         public int getTypeId() { return rawOrderId; }

common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4.java

@@ -139,6 +139,7 @@ public void initEvent(DataEvent event){
 
                     detectorDecoder.translate(dataList);
                     detectorDecoder.fitPulses(dataList);
+                    detectorDecoder.filterTDCs(dataList);
                     if(this.decoderDebugMode>0){
                         System.out.println("\n>>>>>>>>> TRANSLATED data");
                         for(DetectorDataDgtz data : dataList){
@@ -260,6 +261,7 @@ public Bank getDataBankWF(String name, DetectorType type) {
             b.putShort("component", i, (short) a.get(i).getDescriptor().getComponent());
             b.putByte("order", i, (byte) a.get(i).getDescriptor().getOrder());
             b.putLong("timestamp", i, a.get(i).getADCData(0).getTimeStamp());
+            b.putInt("time", i, (int)a.get(i).getADCData(0).getTime());
             DetectorDataDgtz.ADCData xxx = a.get(i).getADCData(0);
             for (int j=0; j<xxx.getPulseSize(); ++j)
                 b.putShort(String.format("s%d",j+1), i, xxx.getPulseValue(j));
@@ -307,8 +309,10 @@ public Bank getDataBankTDC(String name, DetectorType type){
             tdcBANK.putByte("sector", i, (byte) tdcDGTZ.get(i).getDescriptor().getSector());
             tdcBANK.putByte("layer", i, (byte) tdcDGTZ.get(i).getDescriptor().getLayer());
             tdcBANK.putShort("component", i, (short) tdcDGTZ.get(i).getDescriptor().getComponent());
-            tdcBANK.putByte("order", i, (byte) tdcDGTZ.get(i).getDescriptor().getOrder());
+            tdcBANK.putByte("order", i, (byte) (tdcDGTZ.get(i).getDescriptor().getOrder()+tdcDGTZ.get(i).getTDCData(0).getType().getTypeId()));
             tdcBANK.putInt("TDC", i, tdcDGTZ.get(i).getTDCData(0).getTime());
+            if(name == "DC::tdc")
+                tdcBANK.putShort("ToT", i, (short) tdcDGTZ.get(i).getTDCData(0).getToT());
         }
         return tdcBANK;
     }
@@ -332,6 +336,8 @@ public Bank getDataBankTDCPetiroc(String name, DetectorType type){
             tdcBANK.putByte("order", i, (byte) tdcDGTZ.get(i).getDescriptor().getOrder());
             tdcBANK.putInt("TDC", i, tdcDGTZ.get(i).getTDCData(0).getTime());
             tdcBANK.putInt("ToT", i, tdcDGTZ.get(i).getTDCData(0).getToT());
+            tdcBANK.putLong("timestamp", i, tdcDGTZ.get(i).getTDCData(0).getTimeStamp());
+            tdcBANK.putInt("trigger", i, tdcDGTZ.get(i).getTrigger());
             //System.err.println("event: " + tdcDGTZ.get(i).toString());
         }
         return tdcBANK;
@@ -433,6 +439,27 @@ public Bank getDataBankUndecodedSCALER(String name, DetectorType type){
         return scalerBANK;
     }
 
+    public Event getDecodedEvent(EvioDataEvent rawEvent, int run, int counter, double torus, double solenoid) {
+
+        Event  decodedEvent = this.getDataEvent(rawEvent);        
+
+        Bank   header = this.createHeaderBank(run, counter, (float) torus, (float) solenoid);
+        if(header!=null) decodedEvent.write(header);
+
+        Bank   trigger = this.createTriggerBank();
+        if(trigger!=null) decodedEvent.write(trigger);
+
+        Bank onlineHelicity = this.createOnlineHelicityBank();
+        if(onlineHelicity!=null) decodedEvent.write(onlineHelicity);
+
+        Bank decodedHelicity = this.createHelicityDecoderBank(rawEvent);
+        if (decodedHelicity!=null) decodedEvent.write(decodedHelicity);
+
+        this.extractPulses(decodedEvent);
+
+        return decodedEvent;
+    }
+
     public Event getDataEvent(DataEvent rawEvent){
         this.initEvent(rawEvent);
         return getDataEvent();
@@ -838,25 +865,14 @@ public static void main(String[] args){
             while(reader.hasEvent()==true){
                 EvioDataEvent event = (EvioDataEvent) reader.getNextEvent();
 
-                Event  decodedEvent = decoder.getDataEvent(event);
-
-                Bank   header = decoder.createHeaderBank( nrun, counter, (float) torus, (float) solenoid);
-                if(header!=null) decodedEvent.write(header);
-                Bank   trigger = decoder.createTriggerBank();
-                if(trigger!=null) decodedEvent.write(trigger);
-                Bank onlineHelicity = decoder.createOnlineHelicityBank();
-                if(onlineHelicity!=null) decodedEvent.write(onlineHelicity);
-                Bank decodedHelicity = decoder.createHelicityDecoderBank(event);
-                if (decodedHelicity!=null) decodedEvent.write(decodedHelicity);
+                Event  decodedEvent = decoder.getDecodedEvent(event, nrun, counter, torus, solenoid);
 
                 Bank epics = decoder.createEpicsBank();
 
                 decodedEvent.read(rawScaler);
                 decodedEvent.read(rawRunConf);
                 decodedEvent.read(helicityAdc);
 
-                decoder.extractPulses(decodedEvent);
-
                 helicityReadings.add(HelicityState.createFromFadcBank(helicityAdc, rawRunConf,
                     decoder.detectorDecoder.scalerManager));